[[FsTutorial|top]] | [[FsTutorial/Tools|previous]]
== Reference ==
=== 1.0 Mouse commands ===
'''1.1 Mouse clicks''' <
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|| '''Button 1''' || Sets the cursor, drawing it in the new location, and marks the clicked vertex. ||
|| '''Button 2''' || Sets the cursor without drawing it in the new location and unmarks the clicked vertex. ||
|| '''Button 3''' || Clears marked vertices. ||
'''1.1 Mouse controls for zooming''' <
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|| '''Control+Button 1''' || Zooms in, doubling the zoom level ||
|| '''Control+Button 3''' || Zooms out, halving the zoom level ||
=== 2.0 Menus ===
'''2.1 File''' <
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|| '''Load Surface...''' || Loads the main surface information, including main surface configuration. ||
|| '''Load Surface Configuration...''' || Shows a submenu with commands for loading vertex configurations. ||
|| '''Save Surface''' || Saves the contents of the entire surface structure, overwriting the original file. ||
|| '''Save Surface As...''' || Saves the contents of the entire surface structure to a new file. ||
|| '''Load Overlay...''' || Loads a .w or binary volume file into an overlay layer. ||
|| '''Save Overlay As...''' || Saves an overlay layer as a new .w file. ||
|| '''Load Time Course...''' || Loads a binary volume as a time course. ||
|| '''Curvature''' || Shows a submenu with options for loading and saving. ||
|| '''Patch''' || Shows a submenu with options for loading and saving. ||
|| '''Label''' || Shows a submenu with options for loading and saving. ||
|| '''Field Sign''' || Shows a submenu with options for loading and saving. ||
|| '''Field Mask''' || Shows a submenu with options for loading and saving. ||
|| '''Quit''' || Quits tksurfer. ||
'''2.2 Load surface configuration''' <
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|| '''Main Vertices''' || Loads the specified vertices from another surface file into the selected surface configuration. ||
|| '''Inflated Vertices''' ||
|| '''White Vertices''' ||
|| '''Pial Vertices'''||
|| '''Original Vertices''' ||
'''2.3 Curvature''' <
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|| '''Load Curvature...''' || Loads a curvature file. ||
|| '''Save''' || Saves changes to the curvature, overwriting the original file. ||
|| '''Save Curvature As...''' || Saves the curvature into a new file. ||
'''2.4 Patch''' <
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|| '''Load Patch...''' || Loads a patch file. ||
|| '''Save Patch''' || Saves changes to the patch, overwriting the original file. ||
|| '''Save Patch As...''' || Saves the patch into a new file. ||
'''2.5 Label''' <
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|| '''Load Label...''' || Loads a label file. ||
|| '''Save Label''' || Saves changes to the label, overwriting the original file. ||
|| '''Save Label As...''' || Saves the label into a new file. ||
'''2.6 Field sign''' <
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|| '''Load Field Sign...''' || Loads a field sign file. ||
|| '''Save Field Sign''' || Saves changes to the field sign, overwriting the original file. ||
|| '''Save Field Sign As...''' || Saves the field sign into a new file. ||
'''2.7 Field mask''' <
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|| '''Load Field Mask...''' || Loads a field mask file. ||
|| '''Save Field Mask''' || Saves changes to the field mask, overwriting the original file. ||
|| '''Save Field Mask As...''' || Saves the field mask into a new file. ||
'''2.8 Edit''' <
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|| '''Undo''' || Undoes the cut. ||
|| '''Unmark All Vertices''' || Unmarks all vertices. Same as clicking with button 3 in the Graphics window. ||
|| '''Clear Label''' || Clears the vertices selected by loading a label. ||
'''2.9 View''' <
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|| '''Tool Bars''' || Shows a submenu of available toolbars. Check or uncheck the toolbar in this submenu to show or hide the toolbar. ||
|| '''Information''' || Shows a submenu of available information area items such as coordinate labels. Check or uncheck the item in this submenu to show or hide the item. ||
|| '''Configure''' || Shows a submenu of viewing characteristics that can be configured. ||
|| '''Surface Configuration''' || Shows a submenu of surface configurations. Check one to make the currently shown configuration. ||
|| '''Overlay Layer''' || Shows a submenu of overlay layers. Check one to make the currently shown layer. ||
|| '''Overlay''' || Check to display the current overlay layer. ||
|| '''Scale Bar''' || Check to display a scale bar in the window, showing the scale of 10 mm. ||
|| '''Color Scale Bar''' || Check to display a color bar in the Display window, showing the range of colors in the current overlay color scale. ||
|| '''Wireframe Overlay''' || Check to display a wireframe view of the surface edges. ||
'''2.10 Tool bars''' <
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|| '''Main''' || Check to make the Main toolbar visible. This toolbar contains the following controls: Cut Line, Cut Closed Line, Cut Plane, Cut Area, Clear Cuts, Save Point, Goto Saved Point, Restore Home View, Redraw View. ||
'''2.11 Information''' <
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|| '''Vertex Index''' || Check to show the nearest vertex index. ||
|| '''Distance''' || Check to show the distance in mm to the reported index. ||
|| '''Vertex RAS''' || Check to show the RAS coordinates of the vertex. ||
|| '''Vertex Talairach''' || Check to show the Talairach coordinates of the vertex. ||
|| '''MRI Index''' || Check to show the anatomical index of the vertex in the anatomical volume for this subject. ||
|| '''Vertex Normal''' || Check to show the normal vector of the vertex. ||
|| '''Spherical X, Y, Z''' || Check to show the spherical coordinates. ||
|| '''Spherical Rho, Theta''' || Check to show the spherical rho and theta. ||
|| '''Curvature''' || Check to show the curvature value at the vertex. ||
|| '''Field Sign''' || Check to show the field sign value at the vertex. ||
|| '''Overlay Layer 1-5''' || Check to show the overlay layer value at the vertex. ||
|| '''Amplitude''' || Check to show the value at the vertex. ||
|| '''Angle''' || Check to show the value at the vertex. ||
|| '''Degree''' || Check to show the value at the vertex. ||
|| '''Annotation''' || Check to show the value at the vertex. ||
|| '''MRI Value''' || Check to show the MRI value at the associated anatomical location for this vertex. ||
|| '''Parcellation''' || Check to show the name of the parcellation label of this vertex. ||
'''2.12 Configure''' <
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|| '''Lighting...''' || Opens a dialog box in which you can set the lighting parameters for the scene. ||
|| '''Overlay...''' || Opens a dialog in which you can change various characteristics of the overlay display. ||
|| '''Time Course...''' || Opens a dialog in which you can change various characteristics of the time course graph. ||
|| '''Curvature Display...''' || Opens a dialog in which you can change various characteristics of the curvature display. ||
|| '''Phase Encoded Data Display...''' || Opens a dialog in which you can change various characteristics of phase encoded data display. ||
'''2.13 Surface configuration''' <
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|| '''Main''' || Check to make this surface configuration the currently displayed one. ||
|| '''Inflated''' ||
|| '''White''' ||
|| '''Pial''' ||
|| '''Original''' ||
'''2.14 Overlay layer''' <
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|| '''Overlay Layer 1-5''' || Check to make this overlay layer the currently displayed one. ||
'''2.15 Tools''' <
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|| '''Save Point''' || Saves the current cursor so that tksurfer or [[FsTutorial/Tools|tkmedit]] can use its Goto Saved Point function to go to that point. ||
|| '''Goto Saved Point''' || Sets the cursor to the one last saved in tksurfer or [[FsTutorial/Tools|tkmedit]] for this subject. ||
|| '''Run Script...''' || Executes a tcl script. ||
|| '''Cut Line''' || Calculates a line between marked vertices and cuts the vertices in that line. ||
|| '''Cut Closed Line''' || Same as above, but closes the line between the first and last marked vertex. ||
|| '''Cut Plane''' || Requires exactly four vertices to be marked. Cuts the surface but not in the plane defined by the four vertices. ||
|| '''Cut Area''' || Requires one marked vertex and two incontiguous surface areas. Cuts the area that the marked vertex is not in. ||
|| '''Clear Cuts''' || Removes all cut vertex, restoring the surface to whole. ||
|| '''Send to Subject...''' || Same as Save Point, but allows you to enter a subject name explicitly. ||
|| '''Write Decimation...''' || Not functional, reserved for future upgrade. ||
|| '''Write Dipoles...''' || Writes a file containing the dipole values at each vertex. ||
|| '''Set Background Midpoint to Average''' || In the curvature colorscale, sets the point at which red transitions to green to the mean curvature across the whole surface, making the data more interpretable. ||
|| '''Fill Stats''' || Marks vertices based on the overlay values surrounding the cursor. ||
|| '''Fill Curvature''' || Marks the region around each selected vertex that has a similar curvature to that of the selected curvature. Used for labeling anatomical regions. ||
|| '''Smooth...''' || Iteratively smooths scalar for a user-selected number of iterations. Equivalent to convolving with a surface-based gaussian. ||
|| '''Inflate....''' || Applies the inflation force for a user-specified number of iterations, to smooth the surface. ||
|| '''Swap Surface Fields...''' || Intended for use by those who know the internal data structure of the surface. Opens a dialog box allowing you to specify two surface vertex fields to swap. ||
|| '''Clear Curvature''' || Sets the curvature value at each vertex to 0. ||
|| '''Graph Marked Vertices Avg''' || Graphs the average of marked vertices in the time course. ||
|| '''Graph Label Avg''' || Graphs the average of a label in the time course. ||
|| '''Save Graph to Postscript File''' || Saves the contents of the time course graph to a Postscript file. ||
|| '''Save RGB As...''' || Saves the contents of the Display window to an RGB file. ||